Hello everyone. I'm new to Galaxy. We intend to install a local Galaxy Server to process data. But as the first step of the pipeline, we need to use a web App we have already developed. We thought that having the servlet already ready, the Galaxy tool would just need to call the url.

Other approaches I have used before is to use the web app itself to push data into Galaxy - you said servlet so I assume this is something on the JVM - pushing data from an external application into Galaxy is exactly the use case that drove me to initially write blend4j.

Finally, if you have identifiers and a consistent API to your webapp sometimes it is easiest to just write a simple tool to fetch data. Here is an example of such a tool I wrote for the Galaxy-P project awhile ago.